[gmx-users] which force field for a protein-protein complex?
alanwilter at gmail.com
Wed Sep 10 21:07:41 CEST 2008
Short answer, try Amber99SB with Gaff.
> Message: 1
> Date: Fri, 5 Sep 2008 15:06:21 +0200
> From: " Paula Gonz?lez-Rubio " <paula.grg at gmail.com>
> Subject: [gmx-users] which force field for a protein-protein complex?
> To: gmx-users at gromacs.org
> <2408dbb80809050606k52d73eafsd87f6b54987d6713 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> Hello there,
> I would like to do a MD of a protein-protein complex (both with their
> ligands) so I'm looking for some advise regarding the best force field for
> simulate my system. For more details, it consists on a ADP-ribosylase
> ligand is the NAD) and a small G protein (GDP binded), we want to see what
> is the role of a loop in the formation of the complex and on the
> ADP-ribosilation of the small G protein.
> Does any one have a good idea of an appropiate force field for this kind of
> systems ? Do you think gromos 43A1 or ffgmx could be an option?
> Thanks a lot in advance!
> -- !!!!! NEW email !!!!!!
> paula.grg at univ-paris-diderot.fr
> ******* NEW ADDRESS ******
> Paula GONZALEZ-RUBIO
> PhD Candidate
> DSIMB INTS, INSERM UMR-S726
> 6 rue Alexandre Cabanel 75015 Paris
> Tel : +33(1) 44 49 30 00 Fax : +33(1) 47 34 74 31
> 4th Floor. Room 401 Bis
> Web Site: http://www.dsimb.inserm.fr/<
> -------------- next part --------------
> An HTML attachment was scrubbed...
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users